Reconstructions and analyses from the IARPA MICrONS consortium mouse cortex Layer 2/3 serial EM volume.
Attribution: https://www.microns-explorer.org/terms-and-conditions
Citation: https://www.microns-explorer.org/citation-policy
For an intriguing summary of this revolution, read Mitch Glickstein’s essay on Golgi and Cajal in Current Biology.
Pyramidal neuron of the mouse cortex stained using the Golgi method
Image credit: I created this serial LM reconstruction of a Golgi-stained mouse pyramidal neuron using a Zeiss Photomicroscope II at 40x oil and Smart Objects in Photoshop.
Petabytes of data have been generated for small volumes (1 cubic mm or less) of human, mouse, songbird, and fly brain volumes. This gargantuan task has been spearheaded by investigators from a variety of entities, including Allen Institute, Baylor, Columbia, Google Research, Harvard, IARPA, Janelia/HHMI, Johns Hopkins, Max Planck Institute, Princeton, Rice, and the University of Cambridge, among others.
Pyramdial neuron from the Layer 2/3 serial EM volume
Image credit, I created this reconstruction using Neuroglancer of pyramidal neuron with cellid 648518346349538440 in the Layer 2/3 volume.
This github repo focuses on visualization and analyses of the Layer 2/3 EM volume data generated in the IARPA Microns consortium (Allen Institute, Baylor, Princeton). The volume can be viewed in Neuroglancer (developed at Google Research). Allen Institute and the Seung lab at Princeton have posted datasets, resources, analysis tools, and more on their respective github repos, and also at the Allen Brain Map website.
Use lookup_cellid_in_layer23_volume_neuroglancer.ipynb
to identify the cell subtype for a given cellid in the Layer 2/3 volume.
This is a human-curated list for cells that contain all (or most) of the
cell soma within the volume. Includes a Neuroglancer link generator. See
also a version that adds the Neuroglancer nucleus id (for cells with a
nucleus in the volume): lookup_cellid_in_layer23_volume_neuroglancer_with_nucleus_id.ipynb.
Use list_of_cell_subtypes_in_layer23_volume.ipynb
to view the cellids categorized by cell subtype, from a curated list of
619 cellids.
Use lookup_mitochondria_ids.ipynb
to look up mitochondria ids by cellid. Useful for creating a list of
mito ids for visualization in neuroglancer and for analyzing voxel
data.
Use neuroglancer_link_generator_mitochondria_visualization_version.ipynb
to generate a Neuroglancer link for a single cellid and single
mitochondrion from the
pni_mito_cellswskel_v185_fullstats.csv datatable.
Use neuroglancer_link_generator_all_mitochondria.ipynb
to generate a Neuroglancer link for all the mitochondria in a single
cellid of interest pulling the mito ids from the
211019_mitochondria_info.csv datatable.
Use vtk_mitochondria_visualizer.ipynb
to generate a 3D interactive view of all mitochondria in a cell of
interest. Note this method has significant file download and space
requirements compared to using the Neuroglancer viewer. Use vtk_mitochondria_visualizer_with_synapses.ipynb
to add the pre- and post-synaptic sites to the visualization as
well.
Use lookup_synapse_ids.ipynb
to look up synapse ids by pre- and post-synaptic cell ids. Also contains
voxel data.
Use synapse_visualizer.ipynb
to create a 2D and 3D visualization of all pre- and post-synaptic sites
on a cell of interest.
Use vtk_nuclei_visualizer_with_vasculature.ipynb
to create an interactive 3D visualize the cell nuclei in the volume
using vtk and OpenGL. Includes a visualization option to include all
vasculature in the volume.
axon_carrying_dendrite
folder: a partial neuron (soma is not in the volume) with a possible
axon-carrying dendrite.
axon-carrying dendrite
autapses
folder: there are three autapses in the Layer 2/3 volume and many
(24) cases of segmenation errors that are not true autapses.
inhibitory basket neuron autapse
mitochondria
folder: analysis of interesting mitochondrial features in the layer
2/3 volume, including the largest contiguous mitochondrion in an
astrocyte, and the largest number of mitochondria by count in an
inhibitory basket neuron.
large contiguous mitochondria in an astrocyte
astrocyte mitochondria
folder: analytical and visualization notebooks and high resolution
3D renderings of astrocyte mitochondria.
3D rendering of astrocyte mitochondria colored with a voxel size threshold
mitochondria analytics
folder: more in-depth analysis of the structural, spatial, and
positional characteristics of mitochondria in the Layer 2/3 volume.
3D interactive visualization of all mitochondria and synapses in a neuron
most_synapses
folder: reconstructions and synaptic analyses of an excitatory
pyramidal neuron with the most synapses in the volume, along with an
inhibitory basket neuron making the most synapses onto other processes
within the volume.
neuron with the most synpases in the layer 2/3 volume
Pairs of neurons in the Layer 2/3 volume that synapse onto one another
reciprocal_pairs
folder: Martinotti-bipolar reciprocal pair (cell ids
648518346349538179 and 648518346349515986, respectively).
Martinotti-bipolar reciprocal pair
oligodendrocyte_648518346349508279
folder: a beautiful example of an oligocyte in the layer 2/3 volume.
Images of myelination as well as an example of mis-segmentation where a
synaptic bouton from a nearby axon was incorrectly segmented to the
oligodendrocyte cell.
oligodendrocyte myelinating a neuronal process
vtk_nuclei_visualizer_with_vasculature.ipynb:
notebook to create a 3D visualization of cell nuclei in the Layer 2/3
volume. Uses meshparty, vtk, and OpenGL. Here, nuclei from excitatory
neurons is shown in light blue; nuceli from inhibitory neurons in light
red, and nuclei from glial cells are shown in olive green. Vasculature
in the Layer 2/3 volume is shown in light grey.
3D interactive visualization with nuclei colored by cell type and including vasculature
Drop me an email if you have any questions or would like to collaborate. Shawn